miga-base 0.7.6.0 → 0.7.7.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 2b881cdffbe06953931fafa52599b97d7e8b66d17fb37ca3d16d774df4162f23
-  data.tar.gz: 57253881d9af0a362102853d8bd8e876ad8da50f496eff72a77cac0a20fad46a
+  metadata.gz: 3682f50e3efe936ce751cd83cc7945edddb8e1c3ea6e654c4d54f8ea79efbfcb
+  data.tar.gz: a5bc821d8f1b6f55baf495eea28e8783c86c61ffaca2d486e4589b818a60038f
 SHA512:
-  metadata.gz: 39a1a13da018cee4512620b014c140f3a661ee0fe658fd8d1d5d727884116d872bc45b77e23a50045e133c8d901acf51edb5a27ec1706d2c9f0ffb5e96969535
-  data.tar.gz: d34f900c757d290d143846bd77c4d6dc331b7cbfdadea7170c6ca9421dc8b112991c2e664658d11b2e36d312bb0d8e588321e29c97642d968defc580deaa00c9
+  metadata.gz: 23e986949f97ae31498b7310eba666f0fc4b5f3e4ab9d38a135b2934db901449dca70ce74830e4353bb60f2196ce2c195b1bfb20400f884494e9766e58ea5214
+  data.tar.gz: 3857008111b8a65b1fbf09442eb3a657789ebf964769c7805485be57298141c363296b7d2491ef3379726344f07892211d10d4c72fc74a8095bc0eaf00d4e873

data/lib/miga/cli/action/stats.rb

@@ -20,6 +20,10 @@ class MiGA::Cli::Action::Stats < MiGA::Cli::Action
         '--try-load',
         'Check if stat exists instead of computing on --compute-and-save'
       ) { |v| cli[:try_load] = v }
+      opt.on(
+        '--ignore-empty',
+        'If the result does not exist, exit without throwing exceptions'
+      ) { |v| cli[:ignore_result_empty] = v }
     end
   end
 
@@ -27,7 +31,7 @@ class MiGA::Cli::Action::Stats < MiGA::Cli::Action
     if cli[:try_load] && !r[:stats].nil? && !r[:stats].empty?
       cli[:compute] = false
     end
-    r = cli.load_result
+    r = cli.load_result or return
     if cli[:compute]
       cli.say 'Computing statistics'
       r.compute_stats

data/lib/miga/cli/objects_helper.rb

@@ -80,7 +80,9 @@ module MiGA::Cli::ObjectsHelper
       raise "Unsupported result for #{klass}: #{self[:result]}"
     end
     r = obj.add_result(self[:result], false)
-    raise "Cannot load result: #{self[:result]}" if r.nil?
+    if r.nil? && !self[:ignore_result_empty]
+      raise "Cannot load result: #{self[:result]}"
+    end
 
     @objects[:result] = r
   end

data/lib/miga/remote_dataset/download.rb

@@ -99,6 +99,7 @@ class MiGA::RemoteDataset
         @timeout_try += 1
         raise e if @timeout_try >= 3
 
+        sleep 5 # <- For: 429 Too Many Requests
         retry
       end
       doc

data/lib/miga/result/stats.rb

@@ -168,10 +168,9 @@ module MiGA::Result::Stats
       stats[:aai] = [$2.to_f, '%']
       3.times { fh.gets }
       fh.each_line do |ln|
-        row = ln.chomp.gsub(/^\s*/, '').split(/\s+/)
-        break if row.empty?
+        next unless ln.chomp =~ /^\s*(\S+)\s+(.+)\s+([0-9\.e-]+)\s+\**\s*$/
 
-        stats[:"#{row[0]}_pvalue"] = row[2].to_f unless row[0] == 'root'
+        stats[:"#{$1}_pvalue"] = $3.to_f unless $1 == 'root'
       end
     end
     stats

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 6, 0]
+  VERSION = [0.7, 7, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 5, 19)
+  VERSION_DATE = Date.new(2020, 6, 4)
 
   ##
   # Reference of MiGA.

data/scripts/project_stats.bash

@@ -11,6 +11,9 @@ cd "$DIR"
 # Initialize
 miga date > "miga-project.start"
 
+# Execute doctor
+miga doctor -P "$PROJECT" -v
+
 # Index taxonomy
 miga tax_index -P "$PROJECT" -i "miga-project.taxonomy.json" --ref --active
 

data/scripts/stats.bash

@@ -14,7 +14,7 @@ miga date > "$DATASET.start"
 # Calculate statistics
 for i in raw_reads trimmed_fasta assembly cds essential_genes ssu distances taxonomy ; do
   echo "# $i"
-  miga stats --compute-and-save -P "$PROJECT" -D "$DATASET" -r $i
+  miga stats --compute-and-save --ignore-empty -P "$PROJECT" -D "$DATASET" -r $i
 done
 
 # Finalize

data/test/dataset_test.rb

@@ -192,4 +192,9 @@ class DatasetTest < Test::Unit::TestCase
     assert_equal(:incomplete, d.status)
     assert_predicate(d, :active?)
   end
+
+  def test_preprocessing_tasks
+    assert_include(MiGA::Dataset.PREPROCESSING_TASKS, :cds)
+    assert_include(MiGA::Dataset.PREPROCESSING_TASKS, :taxonomy)
+  end
 end

data/utils/adapters.fa

@@ -300,3 +300,16 @@ AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG
 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
 >TruSeq3_UniversalAdapter
 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
+
+>Nextera_PE_PrefixNX/1
+AGATGTGTATAAGAGACAG
+>Nextera_PE_PrefixNX/2
+AGATGTGTATAAGAGACAG
+>Nextera_PE_Trans1
+TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+>Nextera_PE_Trans1_rc
+CTGTCTCTTATACACATCTGACGCTGCCGACGA
+>Nextera_PE_Trans2
+GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG
+>Nextera_PE_Trans2_rc
+CTGTCTCTTATACACATCTCCGAGCCCACGAGAC

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.6.0
+  version: 0.7.7.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-19 00:00:00.000000000 Z
+date: 2020-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons